This package provides function declarations and inline function definitions that facilitate communication between R and the Armadillo C++ library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.1016/j.softx.2025.102087>.

Best subset selection in generalised linear models via continuous optimisation. Reformulates the NP-hard discrete subset selection problem as a continuous optimisation over the hypercube [0,1]^p, solved via a Frank-Wolfe homotopy algorithm with closed-form ridge inner solves. Supports linear (Gaussian), binary logistic, and multinomial regression. For methodological details see Moka, Liquet, Zhu and Muller (2024) <doi:10.1007/s11222-024-10387-8> and Mathur, Liquet, Muller and Moka (2026) <doi:10.48550/arXiv.2603.21952>.

This package implements the Capability-Ecological Developmental Model (CEDM) for longitudinal and multilevel data. The package supports estimation and interpretation of models examining how socioeconomic status (SES), health indicators, and contextual factors jointly relate to academic outcomes. Functionality includes: (1) classification of ecological capability regimes (amplifying, neutral, compensatory); (2) estimation of moderated multilevel models with higher-order interaction terms; (3) causal mediation analysis using doubly robust estimation; (4) random-effects within-between (REWB) decomposition; (5) nonlinear moderation using restricted cubic splines; (6) clustering of longitudinal health trajectories; and (7) sensitivity analysis using the impact threshold for a confounding variable (ITCV) and robustness-to-replacement (RIR) measures. The package is designed for use with general longitudinal multilevel datasets.

Generate project files and directories following a pre-made template. You can specify variables to customize file names and content, and flexibly adapt the template to your needs. cookiecutter for R implements a subset of the excellent cookiecutter package for the Python programming language (<https://github.com/cookiecutter/>), and aims to be largely compatible with the original cookiecutter template format.

Fungi are ubiquitous in Earth's wonderfully diverse ecosystems. The ClassifyITS package aids in the taxonomic classification of environmental internal transcribed spacer (ITS) short-read barcoding data. Unlike previous methods, it employs taxon-specific e-value and percent identity cutoffs at each taxonomic rank from kingdom to species. The package takes a conservative approach and outputs both graphics and user-friendly files to help users manually inspect fungal operational taxonomic units (OTUs) that fail classification at relevant levels (e.g., Phylum). ClassifyITS is based on taxonomic cutoff criteria from "The Global Soil Mycobiome consortium dataset for boosting fungal diversity research" (Fungal Diversity, Tedersoo, 2021, <doi:10.1007/s13225-021-00493-7>) and "Best practices in metabarcoding of fungi: From experimental design to results" (Molecular Ecology, Tedersoo, 2022, <doi:10.1111/mec.16460>).

Plots calibration curves and computes statistics for assessing calibration performance. See Lasai et al. (2025) <doi:10.48550/arXiv.2503.08389>, De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.

Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.

Software which provides numerous functionalities for detecting and removing group-level effects from high-dimensional scientific data which, when combined with additional assumptions, allow for causal conclusions, as-described in our manuscripts Bridgeford et al. (2024) <doi:10.1101/2021.09.03.458920> and Bridgeford et al. (2023) <doi:10.48550/arXiv.2307.13868>. Also provides a number of useful utilities for generating simulations and balancing covariates across multiple groups/batches of data via matching and propensity trimming for more than two groups.

Several causal effects are measured using least squares regressions and basis function approximations. Backward and forward selection methods based on different criteria are used to select the basis functions.

This package provides a new methodology for linear regression with both curve response and curve regressors, which is described in Cho, Goude, Brossat and Yao (2013) <doi:10.1080/01621459.2012.722900> and (2015) <doi:10.1007/978-3-319-18732-7_3>. The key idea behind this methodology is dimension reduction based on a singular value decomposition in a Hilbert space, which reduces the curve regression problem to several scalar linear regression problems.

The c060 package provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models.

This package implements Cragg-Donald (1993) <doi:10.1017/S0266466600007519> and Stock and Yogo (2005) <doi:10.1017/CBO9780511614491.006> tests for weak instruments in R.

Patients Mental Health (MH) status, Substance Use (SU) status, and concurrent MH/SU status in the American/Canadian Healthcare Administrative Databases can be identified. The detection is based on given parameters of interest by clinicians including the list of plausible ICD MH/SU codes (3/4/5 characters), the required number of visits of hospital for MH/SU , the required number of visits of service physicians for MH/SU, and the maximum time span within MH visits, within SU visits, and, between MH and SU visits. Methods are described in: Khan S <https://pubmed.ncbi.nlm.nih.gov/29044442/>, Keen C, et al. (2021) <doi:10.1111/add.15580>, Lavergne MR, et al. (2022) <doi:10.1186/s12913-022-07759-z>, Casillas, S M, et al. (2022) <doi:10.1016/j.abrep.2022.100464>, CIHI (2022) <https://www.cihi.ca/en>, CDC (2024) <https://www.cdc.gov>, WHO (2019) <https://icd.who.int/en>.

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.

Cox model inference for relative hazard and covariate-specific pure risk estimated from stratified and unstratified case-cohort data as described in Etievant, L., Gail, M.H. (Lifetime Data Analysis, 2024) <doi:10.1007/s10985-024-09621-2>.

This package provides a comprehensive collection of datasets exclusively focused on crimes, criminal activities, and related topics. This package serves as a valuable resource for researchers, analysts, and students interested in crime analysis, criminology, social and economic studies related to criminal behavior. Datasets span global and local contexts, with a mix of tabular and spatial data.

Design, workflow and statistical analysis of Cluster Randomised Trials of (health) interventions where there may be spillover between the arms (see <https://thomasasmith.github.io/index.html>).

The primary motivation of this package is to take the things that are great about the R packages flextable <https://davidgohel.github.io/flextable/> and officer <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.

This package implements the Centroid Decision Forest (CDF) as a single user-facing function CDF(). The method selects discriminative features via a multi-class class separability score (CSS), splits by nearest class centroid, and aggregates tree votes to produce predictions and class probabilities. Returns CSS-based feature importance as well. Amjad Ali, Saeed Aldahmani, Zardad Khan (2025) <doi:10.48550/arXiv.2503.19306>.

Extends the functionality of base R lists and provides specialized data structures deque', set', dict', and dict.table', the latter to extend the data.table package.

This package provides a cascade select widget for usage in Shiny applications. This is useful for selection of hierarchical choices (e.g. continent, country, city). It is taken from the JavaScript library PrimeReact'.

Fit a CoxSEI (Cox type Self-Exciting Intensity) model to right-censored counting process data.

These experimental expression data (5 leukemic CLL B-lymphocyte of aggressive form from GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the Cascade one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.

Fitting and inference functions for generalized linear models with constrained coefficients.